<p>Soil microbial communities in the floodplains of the Yellow River’s mid-to-lower reaches play a major part in the floodplain ecosystem, but little is known about how they respond to floods. This study integrated field sampling with laboratory analysis, using high-throughput sequencing and bioinformatic approaches to examine the composition, diversity, assembly mechanisms, and co-occurrence network patterns of bacterial and fungal communities in floodplain soils both before and after flooding, with a focus on elucidating the response mechanisms of soil microorganisms following flooding. This study revealed that flooding significantly altered the composition of soil microbial communities, with an increase in the relative abundance of Chloroflexi, Acidobacteria, and Basidiomycota but a decrease in Ascomycota. Bacterial alpha diversity increased after the flood. Community assembly of both bacteria and fungi became more dominated by stochastic processes post-flooding. Specifically, bacterial communities showed reduced variable selection and increased homogeneous selection, whereas fungal communities exhibited decreased homogeneous selection and increased dispersal limitation. Flooding enhanced the complexity and connectivity of bacterial co-occurrence networks, along with an increase in negative correlations. In contrast, the fungal network complexity remained largely unchanged, but positive correlations were strengthened. The results indicated that floods could affect the composition, diversity, and structure of bacterial and fungal communities. The co-occurrence networks and community assembly patterns of bacteria and fungi have different response patterns to floods.</p>